8-37604901-A-G

Variant names:

• chr8-37604901-A-G
• rs1573266
• ENST00000517714.1:n.136-1482T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517714.1(LINC01605):​n.136-1482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,982 control chromosomes in the GnomAD database, including 21,188 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (21188 hom., cov: 32)
• Consequence: LINC01605 ENST00000517714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 8 publications found

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

LOC105379380 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379380	XR_949685.3	n.272-1482T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000517714.1	n.136-1482T>C		intron_variant	Intron 1 of 4	4
LINC01605	ENST00000784043.1	n.250-1482T>C		intron_variant	Intron 1 of 9
LINC01605	ENST00000784117.1	n.248-1482T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79825 AN: 151862 Hom.: 21153 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.517

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.526 AC: 79916 AN: 151982 Hom.: 21188 Cov.: 32 AF XY: 0.530 AC XY: 39383 AN XY: 74278

African (AFR) AF: 0.471 AC: 19517 AN: 41452

American (AMR) AF: 0.532 AC: 8127 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2884 AN: 5132

South Asian (SAS) AF: 0.545 AC: 2618 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6195 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37250 AN: 67940

Other (OTH) AF: 0.519 AC: 1097 AN: 2112

Alfa AF: 0.540 Hom.: 48194

Bravo AF: 0.519

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1573266; hg19: chr8-37462419;